Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 8500289 DvMF_1045 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Miya:8500289 Length = 397 Score = 363 bits (933), Expect = e-105 Identities = 194/396 (48%), Positives = 274/396 (69%), Gaps = 3/396 (0%) Query: 4 KLEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLS 63 K+E+++L KIFG P++A + G K++I ++T ++GV A+ ++EGEI V+MGLS Sbjct: 3 KIEIRDLTKIFGPVPEKALAMVRAGKPKDEIYKRTKHAVGVNRATFDVDEGEIVVVMGLS 62 Query: 64 GSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTV 123 GSGKST+VR LNRLIEPT G V IDG D+ +S +LR +R++ MVFQ+FAL PH TV Sbjct: 63 GSGKSTLVRCLNRLIEPTDGTVRIDGTDVTTLSVKDLRALRQRTFGMVFQNFALFPHRTV 122 Query: 124 LDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINP 183 L+N +G+E+ G A RR+KA +AL +VGL + A P +LSGGM+QRVGLARALA++P Sbjct: 123 LENAEYGLEVMGAAKATRRDKAAEALARVGLAGWEAARPGQLSGGMQQRVGLARALALDP 182 Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243 DILLMDEAFSALDPLIR +MQDEL++LQ ++TIVFISHDLDEA++IGDRI +M++G V Sbjct: 183 DILLMDEAFSALDPLIRRDMQDELLRLQDDVRKTIVFISHDLDEALKIGDRIVLMRDGAV 242 Query: 244 VQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLL 303 VQVGTP++IL +PA+DYV F VDI++V +A + +RS + GPR+AL+ + Sbjct: 243 VQVGTPEDILTSPADDYVARFVADVDIARVLTAGTVMKRSEAVAVLGVD--GPRTALRKM 300 Query: 304 QDEDREYGYVIERGNKFVGVVSIDSLKAALSQAQGIEAALI-DDPLVVDAQTPLSELLSH 362 ++ +V++R +K VG+V+ D + L+ + AA++ D V P SEL+ Sbjct: 301 RNHAIATLFVLDRNHKLVGLVTADDIVEHLAGGERDLAAIMRTDITTVSTDAPASELIPL 360 Query: 363 VGQAPCAVPVVDEEHQYVGIISKRMLLQALDREGGN 398 + P + V DE + G+I + +LL AL GGN Sbjct: 361 MAGLPHPLAVTDERGRLAGVIVRGLLLGALAERGGN 396 Lambda K H 0.319 0.137 0.378 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 461 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 397 Length adjustment: 31 Effective length of query: 369 Effective length of database: 366 Effective search space: 135054 Effective search space used: 135054 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory